Juranic/music dirschema update (#1328)

* Update music-v2.0.yaml

Add parent directories.

* Update CHANGELOG.md

Update MUSIC directory schema

* Update music-v2.0.yaml

Remove "_R" requirement from lab_processed/fastq/DNA/ and lab_processed/fastq/RNA/ directories

* Docs: Update MUSIC docs

---------

Co-authored-by: Juan Puerto <=>

CHANGELOG.md

@@ -11,6 +11,7 @@
 - Updating documentation
 - Change Upload error output to dataclass
 - Revert deprecation of field YAML files
+- Update MUSIC directory schema
 
 ## v0.0.18
 

docs/music/current/index.md

@@ -33,7 +33,12 @@ Related files:
 | pattern | required? | description |
 | --- | --- | --- |
 | <code>extras\/.*</code> | ✓ | Folder for general lab-specific files related to the dataset. |
+| <code>raw\/.*</code> | ✓ | All raw data files for the experiment. |
+| <code>raw\/fastq\/.*</code> | ✓ | Raw sequencing files for the experiment. |
 | <code>raw\/fastq\/[^\/]+_R[^\/]+\.fastq\.gz</code> | ✓ | The raw un-multiplexed fastq files. |
-| <code>lab_processed\/fastq\/DNA\/[^\/]+_R[^\/]+\.fastq\.gz</code> | ✓ | This is a GZip'd version of the fastq files from whole genome sequencing. |
-| <code>lab_processed\/fastq\/RNA\/[^\/]+_R[^\/]+\.fastq\.gz</code> | ✓ | This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2). |
+| <code>lab_processed\/.*</code> | ✓ | Experiment files that were processed by the lab generating the data. |
+| <code>lab_processed\/fastq\/DNA\/.*</code> | ✓ | Directory containing fastq files pertaining to whole genome sequencing. |
+| <code>lab_processed\/fastq\/DNA\/[^\/]+\.fastq\.gz</code> | ✓ | This is a GZip'd version of the fastq files from whole genome sequencing. |
+| <code>lab_processed\/fastq\/RNA\/.*</code> | ✓ | Directory containing fastq files pertaining to RNAseq sequencing. |
+| <code>lab_processed\/fastq\/RNA\/[^\/]+\.fastq\.gz</code> | ✓ | This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2). |
 

src/ingest_validation_tools/directory-schemas/music-v2.0.yaml

@@ -3,19 +3,38 @@ files:
     pattern: extras\/.*
     required: True
     description: Folder for general lab-specific files related to the dataset.
+  -
+    pattern: raw\/.*
+    required: True
+    description: All raw data files for the experiment.
+  -
+    pattern: raw\/fastq\/.*
+    required: True
+    description: Raw sequencing files for the experiment.
   -  
     pattern: raw\/fastq\/[^\/]+_R[^\/]+\.fastq\.gz
     required: True
     description: The raw un-multiplexed fastq files.
     is_qa_qc: False
   -
-    pattern: lab_processed\/fastq\/DNA\/[^\/]+_R[^\/]+\.fastq\.gz
+    pattern: lab_processed\/.*
+    required: True
+    description: Experiment files that were processed by the lab generating the data.
+  -
+    pattern: lab_processed\/fastq\/DNA\/.*
+    required: True
+    description: Directory containing fastq files pertaining to whole genome sequencing.
+  -
+    pattern: lab_processed\/fastq\/DNA\/[^\/]+\.fastq\.gz
     required: True
     description: This is a GZip'd version of the fastq files from whole genome sequencing. 
     is_qa_qc: False
   -
-    pattern: lab_processed\/fastq\/RNA\/[^\/]+_R[^\/]+\.fastq\.gz
+    pattern: lab_processed\/fastq\/RNA\/.*
+    required: True
+    description: Directory containing fastq files pertaining to RNAseq sequencing.
+  -
+    pattern: lab_processed\/fastq\/RNA\/[^\/]+\.fastq\.gz
     required: True
     description: This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2).
     is_qa_qc: False
-